Plant Physiol. Illumina
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

First published online July 15, 2009; 10.1104/pp.109.139030

Plant Physiology 151:16-33 (2009)
© 2009 American Society of Plant Biologists

OPEN ACCESS ARTICLE
This Article
Free via Open Access: OA
Right arrow OA Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Data
Right arrowOA All Versions of this Article:
151/1/16    most recent
pp.109.139030v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via CrossRef
Google Scholar
Right arrow Articles by Lee, T.-H.
Right arrow Articles by Nahm, B. H.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lee, T.-H.
Right arrow Articles by Nahm, B. H.
Agricola
Right arrow Articles by Lee, T.-H.
Right arrow Articles by Nahm, B. H.
Related Collections
Right arrow The Grasses
BIOINFORMATICS

RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice1,[C],[W],[OA]

Tae-Ho Lee2, Yeon-Ki Kim2, Thu Thi Minh Pham, Sang Ik Song, Ju-Kon Kim, Kyu Young Kang, Gynheung An, Ki-Hong Jung, David W. Galbraith, Minkyun Kim, Ung-Han Yoon and Baek Hie Nahm*

Division of Bioscience and Bioinformatics, Myong Ji University, Yongin, Kyonggido 449–728, Korea (T.-H.L., T.T.M.P., S.I.S., J.-K.K., B.H.N.); Genomics Genetics Institute, GreenGene BioTech, Inc., Yongin, Kyonggido 449–728, Korea (T.-H.L., Y.-K.K.); Division of Applied Life Sciences, Gyeongsang National University, Jinju 660–701, Korea (K.Y.K.); Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790–784, Korea (G.A.); Department of Plant Pathology, University of California, Davis, California 95616 (K.-H.J.); Department of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona 85721 (D.W.G.); School of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea (M.K.); and National Academy of Agricultural Science, Rural Development Administration, Suwon 441–707, Korea (U.-H.Y.)

Microarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. However, there have been no reports, to date, of such a database being constructed for rice (Oryza sativa). Here, we describe the construction of such a database, called RiceArrayNet (RAN; http://www.ggbio.com/arraynet/), which provides information on coexpression between genes in terms of correlation coefficients (r values). The average number of coexpressed genes is 214, with SD of 440 at r ≥ 0.5. Given the correlation between genes in a gene pair, the degrees of closeness between genes can be visualized in a relational tree and a relational network. The distribution of correlated genes according to degree of stringency shows how each gene is related to other genes. As an application of RAN, the 16-member L7Ae ribosomal protein family was explored for coexpressed genes and gene expression values within and between rice and Arabidopsis (Arabidopsis thaliana), and common and unique features in coexpression partners and expression patterns were observed for these family members. We observed a correlation pattern between Os01g0968800, a drought-responsive element-binding transcription factor, Os02g0790500, a trehalose-6-phosphate synthase, and Os06g0219500, a small heat shock factor, reflecting the fact that genes responding to the same biological stresses are regulated together. The RAN database can be used as a tool to gain insight into a particular gene by examining its coexpression partners.

1 This work was supported by the Crop Functional Genomics Center of the Frontier Research Program, funded by the Ministry of Science and Technology (grant no. CG1210 to M.K. and grant no. CG1122 to B.H.N.), by the BioGreen21 Program (grant no. 20070401034008 to Y.-K.K. and grant no. 20090101060028 to B.H.N.), by the Rural Development Administration of the Republic of Korea, and by the Brain Korea 21 Project (grants to T.-H.L. and B.H.N.).

2 These authors contributed equally to the article.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Baek Hie Nahm (bhnahm{at}mju.ac.kr).

[C] Some figures in this article are displayed in color online but in black and white in the print edition.

[W] The online version of this article contains Web-only data.

[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.109.139030

* Corresponding author; e-mail bhnahm{at}mju.ac.kr.

Received March 27, 2009; accepted July 6, 2009; published July 15, 2009.

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
ASPB Publications PLANT PHYSIOLOGY® THE PLANT CELL
Copyright © 2009 by the American Society of Plant Biologists